Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014940.1 Corchorus capsularis cultivar CVL-1 contig14961, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 19389
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:266 original size:2 final size:2

Alignment explanation


    Indices: 259--318  Score: 68
    Period size: 2  Copynumber: 30.0  Consensus size: 2

        249 GAACCCTATG

                                        *       *    *  *                  
        259 TA TA TA TA TA TA TA TA -A TG TA TA AA CTC TT TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA

                                      
        301 TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA

        319 CCATAACAGC


Statistics
Matches: 49,  Mismatches: 7, Indels: 4
        0.82            0.12        0.07

Matches are distributed among these distances:
   1    1  0.02
   2   48  0.98

ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48


Consensus pattern (2 bp):   
TA

Found at i:6270 original size:15 final size:15

Alignment explanation


    Indices: 6233--6270  Score: 58
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       6223 ATTGTGCATC

                   *       
       6233 GCACCATGGTTGTTT
          1 GCACCATTGTTGTTT

                           
       6248 GCACCATTGTTGTTT
          1 GCACCATTGTTGTTT

              *     
       6263 GCGCCATT
          1 GCACCATT

       6271 CACCCTAGCA


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  15   21  1.00

ACGTcount: A:0.13, C:0.24, G:0.24, T:0.39


Consensus pattern (15 bp):   
GCACCATTGTTGTTT

Found at i:10247 original size:2 final size:2

Alignment explanation


    Indices: 10240--10277  Score: 58
    Period size: 2  Copynumber: 19.0  Consensus size: 2

      10230 GAGTATAAAG

                                     *                      *       
      10240 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT TT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      10278 TTATGAGCAC


Statistics
Matches: 32,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:10628 original size:17 final size:18

Alignment explanation


    Indices: 10592--10628  Score: 58
    Period size: 19  Copynumber: 2.1  Consensus size: 18

      10582 TATTAGGCAA

                               
      10592 GAGATAATATTAGGTGTTT
          1 GAGATAATATTA-GTGTTT

                              
      10611 GAGATAATATTA-TGTTT
          1 GAGATAATATTAGTGTTT

             
      10628 G
          1 G

      10629 GATGTTTGGG


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  17    6  0.33
  19   12  0.67

ACGTcount: A:0.32, C:0.00, G:0.24, T:0.43


Consensus pattern (18 bp):   
GAGATAATATTAGTGTTT

Found at i:12001 original size:2 final size:2

Alignment explanation


    Indices: 11996--12028  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      11986 ATAGTGTGTG

                                                             
      11996 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      12029 CAAATTAAAA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:12108 original size:22 final size:22

Alignment explanation


    Indices: 12083--12125  Score: 86
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      12073 TATCACAATC

                                  
      12083 AATCAAATAGCAAGTTATAATT
          1 AATCAAATAGCAAGTTATAATT

                                 
      12105 AATCAAATAGCAAGTTATAAT
          1 AATCAAATAGCAAGTTATAAT

      12126 AATTGTGTAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.51, C:0.09, G:0.09, T:0.30


Consensus pattern (22 bp):   
AATCAAATAGCAAGTTATAATT
Done.